There have been a couple science fiction novels with this premise:

Protector[0] by Larry Niven

David Weber's Dahak trilogy, available as the Empire from the Ashes[1] omnibus

[0] https://en.wikipedia.org/wiki/Protector_(novel)

[1] https://en.wikipedia.org/wiki/Empire_from_the_Ashes

You mean how we know the Earth wasn't seeded with something similar to archeo-bacteria on purpose? We don't but that doesn't solve the problem.

Or how do we know that we, humans, aren't the colonists? Well, all the life we know comes from the same ancestry, including us.

That doesn't solve the paradox though, unless we are quaranteened in a Zoo.